By default, seqtk hpc input.fq will homopolymer compress the input fastq file and also convert it into a fasta file and drop the quality scores. I understand that keeping scores would be complicated as it is not obvious what quality score to keep for the identical consecutive bases being represented with 1, but was wondering if there is any work or ideas around that being done. In my case, keeping the highest quality score in the stretch would make sense.
I know people can use seqtk hpc x.fq | seqtk seq -F '@' to get a fastq file with some fake quality scores, but I was wondering if I can keep the quality scores somehow related to the sequence with the seqtk hpc command.
By default,
seqtk hpc input.fqwill homopolymer compress the input fastq file and also convert it into a fasta file and drop the quality scores. I understand that keeping scores would be complicated as it is not obvious what quality score to keep for the identical consecutive bases being represented with 1, but was wondering if there is any work or ideas around that being done. In my case, keeping the highest quality score in the stretch would make sense.I know people can use
seqtk hpc x.fq | seqtk seq -F '@'to get a fastq file with some fake quality scores, but I was wondering if I can keep the quality scores somehow related to the sequence with theseqtk hpccommand.Thanks